Small Things Considered

Move Over, DNA

by Merry

Two cells of D. radiodurans showing the
distribution of iron (red line) and manganese
(turquoise, purple, blue, and green lines
indicating increasing concentrations).
Credit: See below.

For 50 years, researchers have  mulled over why D. radiodurans is able to survive 100 times more ionizing radiation (IR) than other bacteria, 2000 times more than a human being. Although both DNA and proteins are damaged by IR, DNA was widely regarded as the critical target. That D. radiodurans can suffer 100 double strand DNA breaks per genome suggests an extraordinary DNA repair mechanism. Alas, such a mechanism has not been found.

Attention shifted in 2004 when Daly et al. reported that the most IR-resistant bacteria had 300 times more manganese and three times less iron than the most IR-sensitive ones.

A Letter to the Blog by Franklin M. Harold

Let's Put Organisms Back in the Picture!

Is biology ripe for revolution, or at least for a revision of its attitude to life and the universe? Carl Woese certainly thinks so (Woese, 2004). He argues with some passion that biology has lost its "guiding vision" thanks to a narrow application of reductionist doctrine, and is in danger of becoming merely an "engineering discipline", an applied science whose purpose is to manipulate living things rather than to understand them. Over the years, Brian Goodwin, Stephen Jay Gould, Richard Lewontin, Lynn Margulis and others have made plain their belief that something is amiss in biology as we know it. And for what it's worth, I think so too (Harold, 2001).

For myself, the focus of discontent is the status of organisms, microbes in particular.

Talmudic Question # 17

What if someone discovered a fourth (or fifth, sixth, etc.) domain of life?

When Fungi Ruled the Earth

A rendering of Prototaxites as it may have looked during the early Devonian Period, approximately 400 million years ago. Credit: Mary Parrish, National Museum of Natural History

A gigantic fossil is making news and revitalizing an old debate. Several museums possess specimens of a cylindrical organism named Prototaxites whose tree-like trunks measure up to 8 meters long by 1 meter wide. Prototaxites dated from approximately 420 to 350 million years ago (Silurian-Devonian era) have been collected from five localities.

Their identity has been enigmatic.

Quick, Who Discovered Antibiotics?

If your answer is Alexander Fleming or Selman Waxman, you would be off by about 50 million years.

A Phylogeny for a Kingdom

The November-December 2006 issue of Mycologia is devoted entirely to "A Phylogeny for the Kingdom Fungi," the product of 5 years of work by more than 100 fungal systematists carried out under the umbrella of "Deep Hypha" with the support of the National Science Foundation.

Bacterial Mitosis: What’s Taking So Long?

by Merry & Elio

More often than not, basic cellular phenomena have been deciphered first in bacteria, and then later elucidated in eukaryotic cells. A glaring exception is mitosis which was first described for eukaryotic cells in the 1880's. The corresponding story for bacterial chromosomes has remained uncharacteristically elusive. Truth is, we don't know much about it, although there has been some piecemeal progress. A review was published in 2006. A recent paper approaches the question by looking at how plasmids are partitioned to the daughter cells during division of their host bacterium.

A Friend Has a Birthday

One of the most steadfast friends of this blog, Robert Murray, will soon be honored on his 88th birthday by an honorary degree from McGill University.

Taxa Dollars

"Encyclopedia of Life To Catalogue Species" is the headline in the Washington Post that announces a multi-institutional grant of $12.5 million to list and describe 1.8 million species that have a name (about $7 a species). The estimate is that only 10% of all species fall in this category. From what we're learning about bacteria and archaea, the proportion for "our" organisms is almost certainly much lower. Microbes should get a quantity discount.

Nameless orphaned bacteria
from a lake sediment.

Courtesy of D. E. Caldwell.
Previously published on the
covers of the 2003 issues
of International Microbiology.

Fine Literature: Genome Size Matters

In a recent article in Antimicrobial Agents and Chemotherapy, Steven Projan points out that there is an apparent correlation between the size of a bacterium's genome and its penchant to display multidrug resistance phenotypes.